Source code for drymass.roi

import pathlib
import warnings

[docs]class ROIManagerWarning(UserWarning): """Used for unexpected keyword arguments.""" pass
class ROI(object): def __init__(self, identifier, image_index, roi_index, roi_slice): """Handle one region of interest (ROI)""" if not isinstance(identifier, str): raise ValueError("`identifier` must be a string!") # verify roi_slice if not (isinstance(roi_slice, (tuple, list)) and len(roi_slice) == 2 and isinstance(roi_slice[0], slice) and isinstance(roi_slice[1], slice)): raise ValueError("`roi_slice` must be a tuple of two slices!") self.identifier = identifier self.image_index = image_index self.roi_index = roi_index self.roi_slice = roi_slice def __eq__(self, other): return self.to_str() == other.to_str() def __lt__(self, other): # used for sorting if self.image_index == other.image_index: return self.roi_index < other.roi_index else: return self.image_index < other.image_index def __repr__(self): return self.to_str() @staticmethod def from_str(strin): """Load ROI from a string""" ll = strin.strip().split("\t") # extract slice data sldata = "".join([c for c in ll[3] if c in ",0123456789"]) sldata = sldata.replace(",,", ",").split(",") sldata = [int(s) for s in sldata if s] slice1 = slice(min(sldata[0], sldata[1]), max(sldata[0], sldata[1])) slice2 = slice(min(sldata[2], sldata[3]), max(sldata[2], sldata[3])) roi = ROI(identifier=ll[0], image_index=int(ll[1]), roi_index=int(ll[2]), roi_slice=(slice1, slice2) ) return roi def to_str(self): """Export ROI to a string""" strout = "\t".join([self.identifier, str(self.image_index), str(self.roi_index), str(self.roi_slice) ]) return strout class ROIManager(object): def __init__(self, identifier=None): """Manage regions of interest (ROI) of an image series Parameters ---------- identifier: str or None The identifier of the image series. """ if not (isinstance(identifier, str) or identifier is None): raise ValueError("`identifier` must be `None` or a string!") self.identifier = identifier self.rois = [] def __len__(self): return len(self.rois) def add(self, roi_slice, image_index, roi_index, identifier): """Add a ROI to ROIManager Parameters ---------- roi_slice: (slice, slice) Two slices indicating the x- and y-axis limits. image_index: int The image index of the image series. roi_index: int The ROI index in image `image_index` identifier: str The ROI identifier. If `self.identifier` is not contained within `identifier`, a `ROIManagerWarning` will be issued. """ # verify identifier if not isinstance(identifier, str): raise ValueError("`identifier` must be a string!") if self.identifier and self.identifier not in identifier: msg = "Identifier of ROIManager `{}` ".format(self.identifier) \ + "does not match that of QPSeries `{}`.".format(identifier) warnings.warn(msg, ROIManagerWarning) self.rois.append(ROI(identifier=identifier, image_index=image_index, roi_index=roi_index, roi_slice=roi_slice)) def get_from_image_index(self, image_index): rois = [r for r in self.rois if r.image_index == image_index] return sorted(rois) def load(self, path): """Load ROIs from a text file""" path = pathlib.Path(path) with"r") as fd: lines = fd.readlines() for ll in lines: # ignore empty lines if ll.strip(): self.rois.append(ROI.from_str(ll)) def save(self, path): """Save ROIs to a text file (`path` will be overridden)""" path = pathlib.Path(path) with"w") as fd: for roi in self.rois: fd.write(roi.to_str() + "\r\n")